copy of chapter 16

Griffith called the phenomenon ___________, now defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell.

transformation

These viruses are called _____________ (meaning "bacteria-eaters"), or ________ for short

bacteriophages, phages

A _____________ is little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein

virus

The presence of two strands accounts for the now-familiar term _______.

double helix

Watson constructed such a model, in which the two sugar-phosphate backbones are _________—that is, their subunits run in opposite directions

antiparallel

Given a polynucleotide sequence such as GAATTC, explain what further information you would need in order to identify which is the 5′ end.

You need to know which end has a phosphate group on the 5′ carbon (the 5′ end) and/or which end has an —OH group on the 3′ carbon (the 3′ end)

While trying to develop a vaccine for S. pneumonia, Griffith was surprised to discover the phenomenon of bacterial transformation. Based on the results in the second and third panels of Figure 16.2, what result was he expecting in the fourth panel? Explain

Griffith expected that the mouse injected with the mixture of heat-killed S cells and living R cells would survive, since neither type of cell alone would kill the mouse

In this section, you will learn about the basic principle of ________________, the copying of DNA, as well as some important details of the process.

DNA replication

This _______________ can be distinguished from a conservative model of replication, in which the two parental strands somehow come back together after the process (that is, the parental molecule is conserved).

semiconservative model

The replication of chromosomal DNA begins at particular sites called ______________, short stretches of DNA that have a specific sequence of nucleotides.

origins of replication

At each end of a replication bubble is a ___________, a Y-shaped region where the parental strands of DNA are being unwound

replication fork

________________ are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands.

Helicases

After the parental strands separate, _________________ bind to the unpaired DNA strands, keeping them from re-pairing

single-strand binding proteins

_______________ is an enzyme that helps relieve this strain by breaking, swiveling, and rejoining DNA strands.

Topoisomerase

The RNA chain is called a ______________ and is synthesized by the enzyme _______________

primer, primase

Enzymes called ___________________ catalyze the synthesis of new DNA by adding nucleotides to the 3′ end of a preexisting chain.

DNA polymerases

The DNA strand made by this mechanism is called the _____________.

leading strand

The DNA strand elongating in this direction is called the _____________

lagging strand

These segments of the lagging strand are called ____________, after Reiji Okazaki, the Japanese scientist who discovered them.

Okazaki fragments

Another enzyme, ____________, accomplishes this task, joining the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand.

DNA ligase

In ___________________, other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.

mismatch repair

In many cases, a segment of the strand containing the damage is cut out (excised) by a DNA-cutting enzyme---a _____________---and the resulting gap is then filled with nucleotides, using the undamaged strand as a template

nuclease

There are several such DNA repair systems; one is called _____________.

nucleotide excision repair

Eukaryotic chromosomal DNA molecules have special nucleotide sequences called _______________ at their ends

telomeres

What role does complementary base pairing play in the replication of DNA?

It ensures that the two daughter molecules are exact copies of the parental molecule. When the two strands of the parental molecule separate, each serves as a template on which nucleotides are arranged by the basepairing rules; they will then be polymerized by enzymes into new complementary strands

Identify two major functions of DNA pol III in DNA replication.

DNA pol III covalently adds nucleotides to new DNA strands and proofreads each added nucleotide for correct base pairing

What is the relationship between DNA replication and the S phase of the cell cycle?

In the cell cycle, DNA synthesis occurs during the S phase, between the G1 and G2 phases of interphase. DNA replication is therefore complete before the mitotic phase begins

If the DNA pol I in a given cell were nonfunctional, how would that affect the synthesis of a leading strand?

Synthesis of the leading strand is initiated by an RNA primer, which must be removed and replaced with DNA, a task that could not be performed if the cell's DNA pol I were nonfunctional. In the overview box in Figure 16.18, just to the left of the top origin of replication, a functional DNA pol I would replace the RNA primer of the leading strand (shown in red) with DNA nucleotides (blue). The nucleotides would be added on to the 3′ end of the first Okazaki fragment of the upper lagging strand (the right half of the replication bubble).

The exact way in which this complex of DNA and protein, called ______________, fits into the nucleus has long been debated.

chromatin

The less compacted, more dispersed interphase chromatin is called _____________ ("true chromatin") to distinguish it from the more compacted, denser-appearing ______________(see Figure 16.23).

euchromatin, heterochromatin

Describe the structure of a nucleosome, the basic unit of DNA packing in eukaryotic cells.

A nucleosome is made up of eight histone proteins, two each of four different types, around which DNA is wound. Linker DNA runs from one nucleosome to the next.

How does euchromatin differ from heterochromatin in structure and function?

The 10-nm fiber of euchromatin is less compacted during interphase than in mitosis and is accessible to the cellular proteins responsible for gene expression. In contrast, the 10-nm fiber of heterochromatin is relatively compacted (densely arranged) during interphase, and genes in heterochromatin are largely inaccessible to proteins necessary for gene expression.

Interphase chromosomes appear to be attached to the nuclear lamina and perhaps also the nuclear matrix. Describe these two structures.

The nuclear lamina is a netlike array of protein filaments that provides mechanical support just inside the nuclear envelope and thus maintains the shape of the nucleus. Considerable evidence also supports the existence of a nuclear matrix, a framework of protein fibers extending throughout the nuclear interior.